Hey Chasevida,
I think the more generic question you're asking here is "How do I change the requirement files that are pre-bundled with the CWP recipe code?"
The answer is, overloading methods on the Page.php which inherits from BasePage.php (the underlying page class which is used in CWP to ensure certain features are available in SilverStripe CMS).
Take a look at https://gitlab.cwp.govt.nz/cwp/cwp/blob/master/code/pagetypes/BasePage.php#L462
This is where the group of files are set, and further down the class in the init() method is where they are required and there is a mechanism that minifies and combines these files to improve performance.
By blocking jquery as you have here, you may impact performance of the site once it gets on to a production server.
The better way to approach this would be in Page.php Page_Controller class, to overload the getBaseScripts() method by adding it in your controller and them modifying what is returned.
Just be aware that removing jquery might have impacts elsewhere if there are other jquery plugins used (however if you are rolling your own entire frontend this is likley less of an issue).
As far as the position of the javascript goes... if you properly overload the Requirements as above, it should automatically place the JS in the end of your markup as you are after.
Docs about requirements in general are at http://docs.silverstripe.org/en/developer_guides/templates/requirements/
Interesting that Requirements::clear() isn't working... where about are you putting this?